Variant report

Variant	rs28050
Chromosome Location	chr5:96145424-96145425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96143815..96145603-chr5:96340222..96341890,2	K562	blood:
2	chr5:96142546..96145890-chr5:96269908..96273049,5	K562	blood:
3	chr5:96141925..96145850-chr5:96265867..96272606,9	K562	blood:

Variant related genes	Relation type
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12652636	0.84[ASN][1000 genomes]
rs151928	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs151949	0.97[ASN][1000 genomes]
rs18036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs245478	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26614	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26615	0.94[CEU][hapmap];0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26650	0.94[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs26652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26657	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27543	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27778	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28048	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28049	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs469736	0.94[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs469876	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60432718	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67888194	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28050	ERAP2	cis	cerebellum	SCAN
rs28050	LRAP	cis	multi-tissue	Pritchard
rs28050	ERAP1	cis	cerebellum	SCAN
rs28050	PCSK1	cis	cerebellum	SCAN
rs28050	ERAP2	cis	lymphoblastoid	seeQTL
rs28050	ERAP2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96144400-96147600	Enhancers	Fetal Thymus	thymus
2	chr5:96144400-96151600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:96144400-96152000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:96144600-96146800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:96144600-96147400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr5:96144600-96147600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr5:96144600-96148400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:96144600-96148600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr5:96144600-96151200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:96144600-96151800	Enhancers	Primary T cells from cord blood	blood
11	chr5:96144600-96151800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:96144600-96152200	Weak transcription	Colonic Mucosa	Colon
13	chr5:96144600-96152800	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:96144600-96152800	Weak transcription	Osteobl	bone
15	chr5:96144600-96156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:96144800-96145600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:96144800-96145600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr5:96144800-96145800	Weak transcription	Fetal Heart	heart
19	chr5:96144800-96145800	Weak transcription	Thymus	Thymus
20	chr5:96144800-96146000	Weak transcription	Fetal Lung	lung
21	chr5:96144800-96146200	Weak transcription	Brain Germinal Matrix	brain
22	chr5:96144800-96147200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:96144800-96147200	Weak transcription	HepG2	liver
24	chr5:96144800-96149800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:96144800-96149800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:96144800-96149800	Weak transcription	Fetal Intestine Large	intestine
27	chr5:96144800-96149800	Weak transcription	Fetal Intestine Small	intestine
28	chr5:96144800-96151600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:96144800-96151600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:96144800-96152200	Weak transcription	Placenta	Placenta
31	chr5:96145200-96145600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:96145200-96145600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:96145200-96148600	Weak transcription	Dnd41	blood
34	chr5:96145400-96145800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr5:96145400-96145800	Weak transcription	K562	blood

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